The Chosen Twelve
by maria100
Summary: Atlantis has been infiltrated by twelve wraith worshippers. But with Sheppard injured and explosions rocking the city, it doesn't look good for the Atlantis Expedition. Whumping of a certain main character! Set during season 2.
1. Chapter 1: Coming In Hot

_Disclaimer: I don't own Stargate Atlantis or any of its characters just in case someone wants to sue!_

_Warning: There is strong violence in this story and scenes that some people may find upsetting so ye be warned!_

_Thank you to my beta The Bog Witch who corrected all my mistakes._

The Chosen Twelve

Chapter One: Coming in Hot

Lieutenant Colonel Sheppard slowly walked down the corridor, on his way to debrief with Doctor Weir. He and his team had had an uneventful off-world trip for once where the only danger was that Sheppard might give in to his urges and throttle Doctor McKay.

The ancient technology that McKay had promised was nowhere to be seen and he had complained the whole trip, making the hot, humid planet a lot less pleasant. Sheppard had gladly left his team, including the still complaining McKay, in the infirmary being checked over by the chief medical officer, Doctor Beckett.

Sheppard was crossing his fingers for the lack of excitement in his and everyone else's lives on Atlantis to continue. There had been no wraith or genii activity for a week now and no drama on Atlantis, unless you count McKay being his usual arrogant self, which Sheppard didn't.

All of a sudden a loud claxon sounded, followed by a hasty shout. 'Unscheduled off-world activation!' Sheppard picked up his pace and ran the rest of the way to the control room. He met Elizabeth Weir by the ancient consoles at the top of the stairs.

'What's going on?' He asked Weir impatiently. 'Major Lorne's team are the only ones off-world and they checked in just after I got back.'

Weir nodded calmly. 'I'm well aware of that Colonel, why don't we wait and see.' The seventh chevron locked into place and the wormhole opened with a whoosh.

'We're receiving Major Lorne's IDC.' The technician told the two expedition leaders standing over him anxiously.

'Put me through to his radio.' Weir ordered.

The technician nodded once he had done so. 'Major Lorne, what's your status?' She asked clearly.

The major's voice came back in a rush, he was obviously running hard. 'The wraith have attacked the planet, there are two, I repeat two hive ships bearing down on us. I've just gone back to help the dozen villagers that we were able to save. Permission to bring them back to Atlantis ma'am.'

Weir frowned, the safety of Atlantis was paramount and the less people that knew of its continued existence, the better. 'Can't you dial the alpha site Major?' You know full well that these villagers would be a threat to security here.' Weir's disapproval of Lorne's actions was plain in her voice.

'Yes ma'am I know, Lieutenant Geller dialled the gate, not knowing of the people I had rescued.' He told her, referring to his second in command. 'There's no time to dial the alpha site, the hive ships are overhead.' There was the sound of rapid gunfire over the radio.

Weir looked to Sheppard imploringly. 'What do you think John?'

Sheppard shrugged, 'If they come here, those villagers can never be trusted to leave again. They may tell the wraith that Atlantis isn't destroyed like they think it is… which would be very bad!' He added on seeing Weirs look of confusion.

'I know that!' Weir muttered hastily. 'But that doesn't help me decide what to do.' She sighed. 'I can't leave them there to die. Lower the shield.' She told the technician. She tapped on her radio. 'Major Lorne, you are all clear to come through.'

A few seconds later Major Lorne stepped through with his team, all looking worn out but with no apparent injuries, followed by the twelve villagers that Lorne's team had rescued. Weir sighed, another community wiped out by the wraith she thought sadly to herself. She stepped forward to greet the remaining villagers.

Sheppard gazed distrustfully at the twelve people standing by the gate, his gut telling him that something bad was about to happen. He wanted to grab Weir and tell her to be careful but there was no sign of anything wrong. The villagers looked exactly like they should do, though it was odd that only grown men had survived the culling.

It happened so fast that most people were unaware of what was happening but Sheppard saw it in sickening slow motion. One of the villagers leant forward and grabbed Lieutenant Geller's P90 and the remaining villager's surrounded Lorne's team, leaving them unable to help. The villager pointed it at Weir, who was walking down the stairs, and fired. Sheppard acted immediately.

He threw himself at Weir who was still frozen to the spot on the stairs, staring at the P90 that was pointed at her. The bullet meant for Weir's heart tore through layers of the colonel's clothes and went straight through his shoulder. Sheppard couldn't help the scream that was ripped from his throat. The colonel's momentum pulled the pair down the stairs, Weir too shocked to put a steadying hand out to save herself. Sheppard groaned in agony at the pain in his shoulder hitting each step on the fall down before becoming deathly silent.

The villager with the P90 now had it set to rapid fire and was shooting randomly around the control room. Lorne and his team dove for cover, unable to do anything to help their falling CO's. In the ensuing chaos; the villagers scattered taking any possible exit out of the control room.

Weir and Sheppard finished their bone jarring tumble and Weir whimpered slightly as she strained to sit up. Lorne knelt beside her, supporting her as she swayed. 'Are you alright Doctor?' He asked her, concern evident in his voice.

Weir struggled to her feet. 'I'm fine, just a little dizzy, how's the colonel?'

Geller was knelt over Sheppard. 'Not so good ma'am. You'd better get a medical team down here.'

Weir quickly tapped on her ear piece. 'Doctor Beckett? We need a medical team in the control room right away, Colonel Sheppard has been shot.' Weir turned back to Geller 'Keep an eye on him till Beckett arrives.' She told him. She turned away from Sheppard's still form. She couldn't bear to look at his white face any longer or the blood that was seeping out of his body.

He had saved her life; of that there was no doubt. But she had to concentrate on the problem at hand. She turned to Major Lorne. 'I want all civilians that aren't needed to be confined to their rooms till this is over. Send out armed teams to capture these villagers, using minimal force, if possible. We want to find out why they are here and who sent them. Also this may just be a big misunderstanding and the villagers are just scared and acting in self defence.'

Major Lorne's face showed his disbelief over this theory. Weir continued 'No Major I don't really believe that either but we shouldn't jump to conclusions. You're in charge of military decisions until Colonel Sheppard is back on his feet.'

'Understood ma'am.' Major Lorne said and went off to follow out Weir's orders.

Weir hurried back to Sheppard's side, sending Geller off to report to Lorne. Sheppard's condition hadn't changed but she carried on the pressure on the bullet wound like Geller had been doing.

Doctor Beckett came rushing into the room closely followed by McKay, Teyla and Ronon and a nurse who was wheeling a gurney. 'Where's our patient then?' Beckett asked. Weir beckoned him over. Beckett took note of the blood spilling over Weir's hands, her desperate attempts to slow the bleeding seemed to have failed judging by the amount of blood covering the colonel's clothes and the floor.

'Carson, he was shot in the shoulder and then he fell down the stairs.' Weir hurriedly told him.

'Looks like you took a wee tumble yourself, lass.' Beckett noted, pointing to the large bump forming on Weir's head. He knelt down beside Sheppard and felt for Sheppard's pulse. 'Weak pulse.' He told the group assembled round the fallen colonel. 'Right lets get him back to the infirmary, Elizabeth, you've done a good job I'll take over from there.' He pushed down on the wound and nodded to the nurse to start wheeling the gurney back to the infirmary.

'Will he be o.k.?' McKay asked nervously, jogging after the doctor.

'I'll know more once we get him to the infirmary.' Beckett shouted back to them.

Sheppard's team went to follow Beckett down the corridor but Weir stopped them. 'I know you want to know what's going on with Colonel Sheppard but we have a situation on our hands. We have twelve possibly armed hostiles in Atlantis. Ronon, Teyla, I want you to check in with Major Lorne and join a team tracking down the hostiles. McKay, maybe you can bring up the life signs detector to help them search.'

'What do you mean maybe?' McKay scoffed 'Remember who you are talking to Elizabeth, of course I can bring up the life signs detector, just because I was wrong that one time…'

'Rodney!' Weir tried to interrupt.

'…about that whole ancient weapon-'

'Rodney! Stop! We know you can do it, so go and do it alright?' Weir told him in a tone that left no room for argument.

The three team mates nodded their agreement and left to follow Weir's instructions, careful not to look at the red puddle lining the floor at their feet.


	2. Chapter 2: The Wraith's Plan Laid Bare

_Disclaimer: I don't own Stargate Atlantis or any of its characters just in case someone wants to sue!_

_Warning: There is strong violence in this story and scenes that some people may find upsetting so ye be warned!_

_Thank you to my beta The Bog Witch who corrected all my mistakes._

**Thanks for all the reviews, I went back and fixed Beckett's name in the first chapter and a few other mistakes that I noticed after I put it up. Sorry it wasn't perfect. When I read the reviews it really encouraged me to keep writing. I have the whole story planned in detail; it's just a matter of writing it! Well here's the next chapter. Hope you all enjoy it. Sorry it took so long to get up but the site wouldn't let me post anything. **

Chapter Two: The Wraith's Plan Laid Bare

'I need another unit of blood!' Beckett yelled to the numerous nurses that surrounded him and the prone figure of John Sheppard. 'Get that I.V. set up sharpish please.' He barked to one of the nurses 'The colonel's lost a lot of fluids.'

Becket snapped on a pair of latex gloves. 'Right lets get this bleeding under control.' He nodded to his fellow doctor 'Keep an eye on his blood pressure, the bullet went straight through his axillary artery so we'd best get him sewed back together!'

The nurse handed him a scalpel and the needle. There was no need to sedate the colonel though, Beckett thought sadly, he was so out of it because of shock and blood loss that he wouldn't feel a thing.

'BP's dropping!' the doctor told Beckett, 'Carson, we need to find the source of the bleeding, the colonel's body can't stand much more. We need to get him stabilised.'

Beckett nodded and started to work on Sheppard's wound. The bullet had wrought intensive damage to the insides of Sheppard's body and it was painstaking work for Beckett to fix it. Finally, Beckett looked up at his colleagues and smiled briefly. 'I think we've got it!' He announced. 'Nurse, keep an eye on his vitals and come get me if there is any change. I'm going to check on Doctor Weir's head injury. If I can get her down here that is!'

Half an hour later, Weir finally got round to answering the chief medical officers summons and entered the infirmary. The city was on high alert and most of its resident's were safely ensconced in their own rooms. There was nothing else that she could help with so she asked an SF to escort her down to the infirmary. She smiled grimly to herself, Carson didn't know this but the only reason that she was answering the summons at all was because she wanted to check up on her military leader.

'How's he doing Carson?' She asked once she had spotted the doctor sitting at his desk.

'I'll take you over to him, if you'd like.' Beckett told her. 'But only if you sit on the bed next to his so that I can take a look at that poorly head of yours.' Weir did as she was told and Beckett began to gently probe her bruised head. 'The colonel lost a great deal of blood but I'm sure that we stopped the bleeding in time. He is still unconscious and his blood pressure is still on the low side but I am confident that he will wake up soon enough and be eager to get out of here.'

Weir nodded at Beckett's prognosis and then winced as he prodded a more tender part of her head. 'Of course he will be out of action for a few weeks.' Beckett continued seemingly unaware of the discomfort he was inflicting on Weir. 'I am in no hurry to put Sheppard back on active duty so that he can undo all the good work that I have just done.'

At this, Weir's eyes snapped up. She stared shrewdly at Beckett and glanced over to where Sheppard lay helpless in the hospital bed.

She had the urge to smooth back his hair which was tussled even more than was usual. She knew that Sheppard wouldn't like being grounded at all, he was always a little lost when he had no work to do and never seemed to get very far in the book he had brought with him even though he didn't need to make the book last anymore. He could have another book shipped out on the Dedalus if he bribed the right people.

'Right lass I've finished examining you. You're free to go. I will give you some Tylenol for the headache that you're not telling me about and I want you to come back if it gets any worse but I doubt it will. I think that you were very lucky that you weren't more hurt.' Beckett told her disapprovingly, like it was somehow Weir's fault that she had hit her head.

'Medical emergency!' A female voice sounded over the radio.

'Whose voice was that?' Weir asked sharply. It had sounded like Teyla's but she couldn't be certain.

'I am not sure Elizabeth.' Beckett answered frowning.

'Major Lorne? What's the status of your search teams?' Weir tapped on her earpiece. Her query was met with static.

'Doctor Weir? This is Teyla. Lieutenant Geller has been gravely wounded. We have captured one of the hostiles and require assistance but Major Lorne is not responding.' Beckett nodded to Weir and went to grab his medical bag.

'I'm on my way with some SF's and a medical team Teyla, what's your position?' Weir asked.

'We are by the grounding station near the north pier. Please hurry; the Lieutenant's condition does not look good.'

Weir jogged with the rest of the party, praying that they got there in time to help the fallen Lieutenant. They round the last corner and found Teyla standing over two unmoving men. Her face was somber and she was bleeding from a gash in her forehead, cradling her arm to her chest.

'Lieutenant Geller passed on a few moments ago. I fear that you could not have helped him anyway, Doctor Beckett.'

Beckett checked Geller's pulse and sadly shook his head. 'Nay lass, there's nothing we could have done for him out here; it looks like he has a stab wound that has punctured a lung. I'm sure you tried your best Teyla. Now let's get you on the gurney before you faint on us. You don't look like you're in great shape in the moment.' Beckett helped Teyla to lay down on the gurney at started to look over her injuries.

Throughout this entire exchange Weir stood in shocked silence; disbelieving that Geller had lost his life when just an hour ago he had been valiantly trying to save Sheppard's.

'Ma'am, what shall we do with the prisoner?' One of the SF's asked Weir.

'What?' Weir murmured she had taken no notice of the figure lying next to Geller, unconscious with his hands and feet bound, presumably by Teyla. 'Oh!' She gave her head a little shake, trying to clear it. She couldn't be distracted at a time like this. 'Take him to the brig. I will question him when he wakes up. Guard him until I get there.'

'Yes ma'am.' The SF answered and dragged the prisoner away.

Weir turned back to the medical staff, they were loading Lieutenant Geller's body onto a second gurney. She sighed; she just didn't understand why people had to die. She had never understood the military's attitude toward dying for your country. Some cause that the government had decided was important was not worth needlessly dying for. Now diplomacy on the other hand did make a difference and there was no need to die for it either. She was a diplomat: not a soldier; but diplomacy didn't seem to be needed much in the Pegasus galaxy where the wraith were concerned. But these hostiles were human and Weir was determined to find out what they wanted.

'Ma'am the prisoner is awake.' A voice said in Weir's ear.

'On my way.' Weir replied. She had escorted Teyla to the infirmary and then had tried and failed to contact Major Lorne or his team again. Ronon and his team were the only ones who were still answering their radios. She was just on her way to the control room to see if McKay where the missing soldiers were when she had been called to the brig. She hurried into the room. She acknowledged the SF.

'Has he said anything yet?' She asked.

'No ma'am, he hasn't.' The SF replied, taking up position by the brig's doorway.

'What's your name?' Weir questioned the prisoner.

The prisoner laughed. 'My name is of no consequence when all of us will soon be dead!'

'Why?' Weir asked calmly, pretending that the shocking comment had no affect on her.

'What have we ever done to you? If we have angered you in any way, I'm sure that we can resolve the issue.'

'You have angered our gods, they desire revenge for the wrong that your people have done us.' The prisoner spat this out, as though the words were distasteful.

'Your gods?' Weir probed.

'Yes, others call them the wraith and run from them in fear but we know different. Our gods rid the worlds of evil and have given the chosen twelve the important task of destroying the Atlantian's new outpost.

'New outpost?' Weir wondered out loud. Then she realised. The hostile didn't realise that this was actually Atlantis. The wraith had told him that it had been destroyed by them and he did not doubt this to be true. They must make sure that the 'chosen twelve', as they were calling themselves, did not realise the truth.

Weir turned back to the SF 'Make sure that-' suddenly she was grabbed from behind. The prisoner had his hands through the bars to the cell and the ancient force field had not activated. The hostile held something cold and sharp to her throat. Weir felt the pain as it sliced into her throat.

'The other eleven will complete their tasks given to them by our gods and you and your people will be no more.' The prisoner growled menacingly. 'I could end your pathetic life right here but I think that I will make you wait to be killed with the rest of your doomed race, knowing that there is nothing you can do to save yourselves!' He let her go and she fell to the floor in a huddle.

'Are you alright ma'am, I'm so sorry I forgot to raise the shield when I put him in the cell and I couldn't get a clear shot to help you!' The SF apologised profusely, knowing that his job was on the line if they got through this situation. He helped Weir to her feet. 'Should I help you to the infirmary?'

'No stay and guard the prisoner and please raise the shield! I will send someone down with a tranquilliser dart so that you can disarm him.' Weir gasped, her neck was sending shooting pains up and down her body and she could feel blood running down her neck.

'What are you going to do about what the prisoner said? He's going to try and destroy Atlantis!' The SF said under his breath so that the prisoner couldn't hear, the worry was clear in his voice.

'I don't know.' Weir admitted. If only Sheppard was able to help she thought desperately.


	3. Chapter 3: Hunt or be Hunted

_Disclaimer: I don't own Stargate Atlantis or any of its characters just in case someone wants to sue!_

_Warning: There is strong violence in this story and scenes that some people may find upsetting so ye be warned!_

_Thank you to my beta The Bog Witch who corrected all my mistakes._

**Here's the next chapter, I didn't get much response from the last chapter so I hope people are still enjoying this. **

Chapter Three: Hunt or be Hunted

Sheppard slowly came back to consciousness. He first noticed the high pitched beeping of a heart monitor. The next thing that he became aware of was the detached way his mind was drifting from his body.

Yep, he thought, Beckett's pumped me full of strong pain meds!

He tried to focus on the infirmary when he felt his mind switching off again, he heard faint murmuring in a bed near him and he concentrated on it, willing his eyes to open.

'You shoulda called me down to you, Elizabeth; you are in no condition to be wandering around the base!' The doctor's thick Scottish brogue penetrated the Colonel's fuzzy head.

'I'm fine Carson.' Weir's voice sounded strange as if she was straining to get the words out.

Sheppard weakly turned his head towards the voices and once again commanded his eyes to open. His body finally obeyed him and he was not happy with what he saw. Weir was lying on the hospital bed next to his and Doctor Beckett was administering first aid to whatever injury she had sustained.

Sheppard felt even worse than he had moments before. He had failed to save Weir from being hurt by the villager and had ended up getting hurt himself as well! That wasn't what he had intended in the millisecond of planning that he had done before jumping into the path of the bullet.

He tried to get the pair's attention, thinking up some wise crack about being in the infirmary again but all he managed was a croak, his voice not co-operating.

It did the job though, Beckett hurried to his side and Weir hopped off the bed and joined the doctor. Beckett looked like he had some quibble with this but decided to give Sheppard his full attention at this time.

'How are you feeling Colonel? You had us all a bit worried for a time.' Beckett gently questioned. 'Is there any pain?'

Sheppard croaked again and Weir hurried to hold a drink to his mouth. Sheppard sucked the water gratefully through the straw that she put to his lips.

He tried to speak again. 'Thanks.' He looked up at her, meeting her concerned gaze. His eyes drifted downward to the stark white bandage covering her throat. This injury had not been caused by the attack that he had saved her from which meant that she had been attacked again whilst he had been unconscious.

Anger coursed through him, giving him a much needed adrenalin boost. 'What happened?' He demanded, struggling to sit up with one arm. The other was immobilised, held in place with a tight sling. He dismissed this new information and concentrated on Weir. She had a large purple bruise on her forehead and a small amount of blood seeping through the bandage on her throat.

'John calm down!' Weir insisted.

'Lay down lad, you will pull out your stitches!' Beckett bellowed. 'Elizabeth will explain everything that's going on if you stop wriggling around!'

Sheppard stopped at the doctor's words, mainly because his energy burst was about spent. Also, he was intimated by Beckett, who could be extremely ferocious when his patients weren't doing as they were told, as he had found out on numerous occasions.

'Fine.' He muttered exhaustedly 'Just tell me what happened. The villagers-'

'John!' Weir stopped him, her voice scratchy and exasperated. 'We have a situation on our hands which I will tell you about, if you will let me!'

Sheppard nodded and winced at the pain it sent rushing through his shoulder.

'Well there were twelve hostiles that came through the gate; one took Lieutenant Geller's gun-'

'Yes, about that, I'll have a word with Geller later, it should never have happened!' Sheppard interrupted.

Weir's eyes filled with tears. 'John,' her voice broke on saying that simple word. She didn't know how to tell him that another man under his command had lost their life.

She didn't need to however as Sheppard had figured it out from her face. 'How did it happen?' He asked his voice thick with anguish.

'The hostiles are loose in the city; we have search teams looking for them. Teyla and Geller managed to capture a hostile but were both hurt. Geller,' here she paused and took in a shaky breath 'Geller was stabbed by the hostile and suffered a punctured lung. The medical team were not able to reach him in time.'

'And Teyla?' Sheppard prompted.

'Son, you may want to look to your left!' Beckett suggested.

Sheppard carefully did as he was told and saw an unconscious Teyla in the bed next to him. 'Will she be alright?' He asked.

'Her arm is broken and she has a concussion. I've sedated her so that she can get some rest.' Beckett informed him.

'Right o.k. but that still doesn't explain how _you_ _were injured_ Doctor Weir!' Sheppard noted sarcastically but there was no humour in his voice.

Weir thought for a second about how to phrase her next sentence. Sheppard wasn't going to be happy about what happened. 'I was integrating the prisoner and I got a little close to the bars.' Weir explained simply.

Sheppard frowned 'But that shouldn't be a problem unless the shield wasn't activated!' Weirs guilty face gave her away. 'Which SF was guarding the prisoner at the time? Come on Elizabeth, don't protect him!'

'Now's not the time John!' Weir told him sharply. 'It was an accident but I'm fine. Now I managed to get some information out of the prisoner.' Weir quickly filled her chief military officer in on the wraith's plans.

'Damn, I hate those pesky wraith!' Sheppard muttered to himself. He turned to Beckett. 'Can you get Major Lorne down here? I'll need to brief him on strategies to capture or kill the remaining hostiles.'

Beckett and Weir exchanged a resigned look. 'Er, we weren't going to tell you but Major Lorne has been out of contact for well over an hour.' Weir admitted.

'Weren't going to tell me? Why not?' Sheppard asked angrily. He was sitting up again, trying to untangle himself from all the wires and tubes that he was hooked up to.

'Calm down Colonel, we didn't tell you because we knew you would act like this!' Beckett told him harshly. 'You're not helping anyone by thrashing about like this!'

Sheppard ignored him and swung his legs over the side of the bed. 'Who's been making the military decisions?' He demanded.

'Ronon and me.' Weir informed him. 'The rest of the military team are out of radio contact. We presume they have been captured by the hostiles.'

'Can't Rodney use the life-signs detector to find them?' Sheppard wondered.

'Yes he is doing that, however I haven't had the chance to go back and check on his progress.' Weir explained. 'If I'm free to go Doctor I will go and check on him now?'

'Yes as long as you take it easy. I'm expecting you to rest though after this crisis is over.' Beckett told her.

'And I'm coming with you.' Sheppard stated, easing himself off the bed.

'You are not!' Beckett and Weir said in unison.

Sheppard's legs buckled as soon as they hit the floor. He would have fallen except for the fact that Beckett grabbed him by his uninjured arm; it still sent tremors through his body to his other shoulder.

'O.k.! Not going!' Sheppard grunted, letting Beckett and Weir help him back onto the bed.

'You lost a great deal of blood Colonel!' Beckett explained. 'You're body needs time to recover.'

'John, just stay put. I will keep you posted.' Weir promised.

Sheppard nodded and settled back more comfortably on his pillows. Weir frowned; she had been expecting more of a fight than this. She couldn't help but feel that he was planning something.

XXXX

'Rodney? How's it going?' Weir asked when she reached the control room.

'Finally!' McKay exclaimed. 'I asked you to come up ages ago! What do you think that I didn't mean it? I know that it's hard to believe that I could possibly need help but what could be more important than what I am doing here?' McKay finally looked up from his laptop. 'Oh God, what happened to you?'

Weir sighed, she really wanted to curl up in a ball in her bed at the moment but she realised a long time that you don't always get what you want. 'I'm fine Rodney! What's your status?'

'Well some of the consoles were damaged when the control room was shot up. This ancient technology isn't infallible, you know!' McKay told her.

'Can you fix it?' Weir asked shortly.

'How many times-' McKay started angrily.

'Yes or no Rodney!'

'Yes! Eventually! That's the problem, I needed you to tell Zelenka to get up here because you told all civilians to stay in their rooms and he won't come up here to help me without your permission. With his help, I will get done in no time. Not that I need his help, I am the best scientist here it's just that I can only do one thing at a time, you know!'

'Alright! I will send Zelenka up here.' Weir told him, he nodded absently and went back to his work, ignoring Weir in favour of his laptop.

XXXXX

After a long and painful walk, Sheppard finally made it to the brig. He had spent more time resting against the wall than actually walking but he went as quickly as possible, knowing that Beckett would soon notice that he was gone from his bed. The chief medical officer was annoyingly thorough at his job. The SF immediately stood to attention when he saw his CO and knew better than to question the Colonel about whether or not he should be there.

'At ease soldier.' Sheppard commanded, a little more sharply than was necessary.

The SF did as he was told, nervously waiting for possible repercussions for his lapse earlier.

'What the hell happened?' Sheppard demanded. He may have seemed more threatening if he wasn't swaying dangerously on the spot.

The SF tactfully ignored this 'I messed up sir! It won't happen again sir!' He answered dutifully.

Sheppard surveyed the soldier thoughtfully. He would have to be punished, that was the military way but he would be lenient because Elizabeth had asked him to.

'What's the status of the prisoner?' He asked, changing the subject.

'He is unarmed Colonel and he woke a few moments ago from the tranq dart.'

'Is the shield raised?'

'Yes sir!' The SF smiled inwardly, he would have been foolish to make the same mistake twice.

'Alright, get me a chair; I'm going to question the prisoner.' Sheppard ordered, grabbing the doorframe for support with his free arm.

'Yes sir.'

XXXXX

'Elizabeth, we have a wee problem!' Beckett's voice came over the radio.

Weir turned away from McKay and Zelenka who were arguing over which wire should be crossed with which wire so that she could hear Beckett. 'What is it now?' She asked irritably.

'Colonel Sheppard has left the infirmary. I won't ask any of my staff to search for him without military protection.' Beckett explained apologetically.

'I understand Carson. I think I know where he is, I will escort him beck to you!' Weir promised. Damn that Colonel, why could he never do as he was told!

'Colonel Sheppard!' Weir exclaimed when she saw him sitting next to the brig. 'I thought I'd find you down here, would you care to explain yourself?'

Sheppard frowned at her and shook his head, motioning to the prisoner who she now saw was watching with keen interest. She shuddered when she remembered the feel of the cold metal digging into her throat and the man's gloating voice, whispering into her ear.

Sheppard guided her out of the brig and she noticed that he was leaning heavily on her. Once the brig doors had shut behind them, Weir turned to Sheppard. 'John, what are you doing up?' She asked softly. 'You're not strong enough!'

'I know that!' He grunted, his legs were giving way beneath him and he was pulling Weir down with him. Weir carefully wrapped her arm around Sheppard's waist and she guided them down the hallway back in the direction of the infirmary. It was a sign of how much pain Sheppard was in that he didn't even argue with where he was being taken.

The pair made slow, silent progress down the corridor. Sheppard was concentrating fully on putting one foot in front of the other and not fainting, or passing out as McKay preferred to call it.

Suddenly, Sheppard got the feeling that they were being followed, he had that hunted feeling, and he had learnt to follow these feelings over the years.

'Elizabeth…' he mumbled breathlessly.

'We're almost there John!' Weir told him encouragingly even though they were nowhere near.

'No Elizabeth, we have to stop!' Sheppard demanded weakly. 'We are being followed! Lean me against the wall. Did you bring a gun?' Sheppard questioned.

'No.' Weir admitted sheepishly.

Sheppard groaned, when would that women learn? He pulled his 9mm of its holster, wishing for the feel of his larger, more powerful P90. His mind wasn't working well and there was no cover in the corridor. He hoped they could surprise the hostile when he came round the corner.

'Stay behind me.' He ordered Weir.

He heard the sound of footsteps and knew that once again his gut feeling had been right.

He saw the hostile run round the corner and before his slower than usual reactions could shoot, he was knocked to the floor, the handgun spinning out of his hand and sliding across the floor, out of reach.

He shoulder protested agonisingly but adrenalin soon kicked in and started fighting the larger figure on top of him.

The hostile punched him in the stomach and knocked the wind out of him, Sheppard's fist connected painfully with the man's jaw.

A shot rang out from behind the fighting pair and the hostile slumped, dead on top of Sheppard.

He looked up to see Weir standing over him, worry lines visible on her forehead. He looked down to see his 9mm clutched tightly in her hand.

'Are you alright?' He asked her, quite sure that this was the first time that she had ever killed anyone.

'Shouldn't I be asking you that?' Weir asked wryly.

'Maybe!' Sheppard admitted. The adrenalin was fading and the pain was coming back. 'He just punched me up a bit. Thanks for shooting him!'

Weir pulled the hostile off of Sheppard. 'I didn't want to but-' she broke off with a gasp. The man had a bloody knife in his hand and there was a spreading stain across Sheppard's stomach.

Sheppard lifted his head slightly and saw his new wound. 'Oh crap!' He croaked 'It wasn't a punch!' He then promptly lost consciousness leaving Weir alone with him and far from any help.

**I will be putting the next chapter up hopefully at the end of the weekend. Please review if you have time as it only takes a few seconds and it means so much to me.**


	4. Chapter 4: Explosive Situations

_Disclaimer: I don't own Stargate Atlantis or any of its characters just in case someone wants to sue!_

_Warning: There is strong violence in this story and scenes that some people may find upsetting so ye be warned!_

_Thank you to my beta The Bog Witch who corrected all my mistakes._

**Thank you for all the response I got to the last chapter, it's weird how much it helps. I was ready to give up on the story after the second chapter because I thought that no-one liked it! We are hotting up to the end of the story now, just a few chapters to go. Hope everyone enjoys it!**

Chapter Four: Explosive Situations

The hallway was as silent as the grave, except for the Weir's panting breath. She knew she was panicking, but she couldn't seem to calm down. Another hostile could come along at any moment and she was sitting on the floor watching her friend bleed to death in front of her.

It was so frustrating; her mind was fighting itself, disgusted that she had actually killed that man who was lying next to the colonel.

Her mind tried to shut down, no longer willing to do anything that she told it to. Weir knew the symptoms, she was going into shock.

_Oh no you don't!_ Weir told herself angrily. If she did nothing, Sheppard would die, that was fact and she refused to have another person's death on her conscience. At that thought her mind snapped into action. She hurriedly grabbed Sheppard's 9mm and tucked it into the waistband of her trousers. Weir then surveyed Sheppard anxiously. The stab wound didn't really seem to be bleeding that heavily anymore but it was probably best to get him to the infirmary as quickly as possible.

Getting him there would be a quandary, however. She wouldn't be able to lift him, even though he was just skin and bones. This meant that the only option she was left with was dragging him.

She thoughtfully looked at Sheppard's strapped up shoulder. Well that decided it, she thought grimly, picking up Sheppard's legs. Despite the gravity of the situation, Weir had the urge to laugh. This was definitely not the most dignified way to travel. She doubted that Sheppard would see the humorous side of the situation but it wasn't like she had a choice, what with the stitches in his shoulder.

She strained to pull Sheppard's deadweight down the corridor. It was physically exhausting and she was concentrating so fully on her task that she didn't hear the footsteps behind her.

'Doctor Weir?' A gruff voice said behind her.

She spun round sharply and was relieved to see Ronon standing with one of the soldiers.

'Do you require assistance?' Ronon asked, gazing down at the unconscious Colonel.

'Yes Ronon, we need to get Colonel Sheppard to the infirmary.' Weir rushed, grateful that she was no longer on her own with Sheppard as she wouldn't know what to do if his condition got any worse.

Ronon didn't need to be told twice. He easily picked Sheppard up, holding him carefully with one arm under Sheppard's injured shoulder and the other under Sheppard's knees. He then set off at a smart pace towards the infirmary, Weir falling in behind and the soldier going last so that he could guard their six.

This went on for a few minutes until Ronon abruptly stopped. Weir instantly went to see what the problem was.

'Put me down this second, Ronon, that is an order!' Sheppard said through gritted teeth.

'John, nice to see you back with us!' Weir said brightly.

'If you don't like how I am holding you, you should have seen how Weir was moving you!' Ronon mentioned, trying to wind up his team leader.

'But you were carrying me like a baby! Could you not think of a more manly way to hold me? Not put me down!' Sheppard commanded, glaring at the Satedan.

'As you wish Sheppard.' Ronon said simply, placing Sheppard on the floor. Sheppard swayed dangerously and would have fallen except for Ronon's steadying hand. Ronon grinned, his point, that Sheppard had needed him, proved.

'Alright, you can wipe that look off your face!' Sheppard said to the taller man. 'I just need to get my bearings!'

Sheppard turned to face Weir. 'Elizabeth, I didn't get the chance to tell you before but I got some new information out of the prisoner, which you're not going to like.' Sheppard had let go of Ronon and was standing on his own. 'The 'Chosen Twelve' were all given an explosive device that they were told to place in different parts of the outpost and detonate within four hours of when they got here.'

'But John, that's half an hour away and there are still ten hostiles out there.' Weir gasped.

'Six,' Ronon grunted. 'Smith and me took out four of the hostiles already.'

'Oh!' Sheppard exclaimed. 'Nice work!' He told Ronon and the soldier who was still guarding their six.

'That still leaves six hostiles with bombs!' Weir noted, unsure of how they could overcome this new problem.

'McKay to Weir.'

'Yes Rodney?' Weir answered the radio transmission.

'I managed to fix the biometric sensor, with some inconsequential help from Radek.' There were some sharp Czech words in the background at this last point.

'How many times do I have to tell you that you need to speak English! I don't have the time nor the inclination to learn such a pointless language. Though of course I could if I put my mind to it, being a genius and all.' McKay said smugly.

'Hah, genius! You couldn't even work out how to bypass the Atlantian's safety control so that we could hook the biometric sensor up to a naqahdah generator!' Zelenka scoffed.

'Oh please, like you worked it all out by yourself!' McKay retorted sarcastically.

'Gentlemen! We don't have time for this.' Weir interrupted the heated argument. 'Is the life sensor fixed and working?'

'Yes Elizabeth of course it works.' McKay answered.

'Could you find any of the hostiles or our missing soldiers?'

'Yes it was quite easy Doctor Weir. There are over fifty people locked in the gym. Rodney believes it can be opened from the outside.' Zelenka informed her.

'What about the hostiles?' Sheppard asked shortly. He was well aware that they were fast running out of time.

'Sheppard!' McKay exclaimed. 'Hasn't Elizabeth carted you back to the infirmary yet?'

'Just answer the question McKay!' Sheppard growled.

McKay was more relieved than he would ever admit to hear Sheppard's voice. 'Fine, there are six life signs where they shouldn't be. Two by the east pier, near the gym, two by the north pier, there is another directly below us in a room under the control room and there is one by the living quarters.' McKay told them.

'Thank you Rodney, we'll get back to you if we need help.' Weir signed off.

She turned to the three men standing round her. 'Right first things first. John we need to get you to the infirmary.'

'Like hell!' Sheppard growled. 'Elizabeth you need me! Atlantis will be destroyed otherwise.'

'He's right.' Ronon agreed reluctantly. 'I will bind his wound up. He will be alright until this crisis is over.'

Weir could see that she wasn't going to win this fight. 'Fine, but I go with you Colonel.' She demanded.

'Fine.' Sheppard agreed easily. He leaned against the wall, lifting his shirt so that Ronon could administer first-aid. He hissed slightly as the shirt caught where the material had stuck to the drying blood of his wound.

'Right here's the plan.' Sheppard told them as Ronon wrapped the bandage tightly around his middle. 'Smith, you head off to the north pier and take out the two hostiles. Ronon, you take out the ones in the control tower and the living quarters, I don't need to tell you how much damage a bomb would do in those areas. Elizabeth and I will go take out the ones on the east pier and let Major Lorne and the others out of the gym as well. Ask McKay the exact position of the hostiles once you're nearer.'

Ronon finished securing the bandages and nodded to Sheppard to show that he understood his orders. 'Right move out, oh no wait!' Sheppard said as Ronon and Smith began to leave. 'Does anyone have any Tylenol?'

Weir frowned. 'What for?' Then she realised. 'Really John, you're not really suggesting taking Tylenol for a stab wound?'

'Why not?' Sheppard said defensively. He took the tablets offered to him by Smith and gulped them down without water. He smiled at Weir cheekily. 'It may take the edge off the pain.'

'Is it that bad John?' Weir asked sympathetically.

Sheppard frowned at what he heard in her voice, he hated people feeling sorry for him. 'I've felt worse.' He said honestly.

Weir could tell he was being truthful and thought back to the whole bug stuck to neck incident and just a few months ago when he had almost turned into a bug/wraith creature. Sheppard had gone through a lot of pain in his career.

'Right move out, good luck!' Sheppard said to Ronon and Smith. They all set off, Smith jogging to get to the north pier on time. Sheppard thought back to when the hurricane had hit Atlantis and McKay had sent him off on the journey to the north pier. Oh well, that's why it was good being in charge, so that he could delegate.

Sheppard set out with Weir to the east pier. 'Elizabeth, I think it's time to give me back my gun now.' He suggested.

Weir gladly gave the deadly weapon back, relieved to be rid of it. She noted how tense Sheppard was and how clenched his jaw was. 'How are you still on your feet John?' Weir asked gently. 'You could hardly stand before, when we had left the brig…'

'It's called adrenalin Elizabeth.' Sheppard said shortly, saving his energy for walking. 'Atlantis needs me to be up and moving, so I am. I'm sure Carson will be keeping me in the infirmary indefinitely after all this is over,'

'I think you're probably right about that, after your stunt this morning! Carson doesn't like being disobeyed.' Elizabeth commented.

They finally arrived at the gym, where Sheppard spared so often with Teyla. He passed his hand over the switch but it didn't open.

'McKay! The damn door won't open!' Sheppard shouted angrily into his radio.

'Won't it? Oh they must have sealed it somehow, has the switch been tampered with?' McKay asked.

'That's an affirmative, Rodney.' Weir answered, looking at the wires hanging out of the switch that Sheppard was trying to activate.

'That's great, just great!' McKay moaned.

Sheppard paced impatiently. 'Elizabeth, I'm gonna have to go on to find the hostiles. Will you be o.k. here by yourself?'

'Yes John, you go. I'll be fine.' Weir told him.

Sheppard quickly set off again, knowing that the four hours were almost up.

'Colonel Sheppard, the hostile is ten metres in front of you, just round the corner.' Zelenka said, over the radio.

'Understood.' Sheppard replied quietly.

He quickly had visual on the hostile who had no idea that Sheppard was behind him. The hostile was leaning over some kind of device, obviously getting ready to arm it. Sheppard didn't give him the chance to do this, however.

He got as close as he could to the hostile and fired a bullet straight into the man's head. He was dead instantly, his body slumped over the device that he had never got the chance to use.

Suddenly the floor shook violently beneath him and Sheppard had to grab the wall for support. A second later, frantic alarms began to sound throughout the city.

**Not another cliffy! Well if people have time would they be able to review as it does give me the motivation to write the next chapter. Thanks and hope to get the next chapter up a bit quicker than this one.**


	5. Chapter 5: Eleven Down, One to Go

_Disclaimer: I don't own Stargate Atlantis or any of its characters just in case someone wants to sue!_

_Warning: There is strong violence in this story and scenes that some people may find upsetting so ye be warned!_

_Thank you to my beta The Bog Witch who corrected all my mistakes._

**Thanks for all the reviews again, this story is almost finished. I'm slightly ahead of myself so the chapters will hopefully be coming quicker! Oh there is a spoiler to the film Titanic below (seriously, I worked in a reference to one of my favourite films!) so if you haven't watched it yet and intend to, you may want to look away!**

Chapter Five: Eleven Down, One to Go!

'McKay, dammit! McKay answer!' Sheppard demanded into his radio. The Atlantian alarms were still clanging and were causing a pounding pain in Sheppard's head. Causing him even more pain was the fact that he didn't know why the alarms had gone off in the first place because McKay wasn't answering Sheppard's frantic calls.

The vibrations in the floor stopped as soon as they had started and Sheppard was convinced that it'd been caused by an explosion, the only question was where the detonation had taken place.

'What is it Sheppard? I'm slightly busy saving all our lives again, here!' McKay moaned, full of self-pity, which was usual in situations like this.

'Could you fill me in? I kinda need to know the status of the base. Where was the explosion? I'm guessing not the control room as you're still talking to me!' Sheppard asked hastily.

'Well done Sheppard for once again proving how unintelligent the military is! No it's not the control room,' McKay said arrogantly, he loved discussing how clever he was compared to Sheppard, conveniently forgetting that Sheppard had passed the Mensa test. 'If it was, Atlantis would already be filling with water.

'The explosion was on the north pier. Sergeant Smith had only taken out one of his hostiles so we can safely assume that it was the other hostile on the north pier!'

'What does Smith have to say about it?'

'He's not answering his radio; he may have been caught in the blast.' McKay said, without emotion. The Atlantis expedition seemed to be becoming desensitised to death as they had seen so much of it.

Sheppard filed that piece of information away for later, there was nothing he could do for Smith at the moment and he still needed to save Atlantis. 'Atlantis is alright then? There'll only be minimal damage surely?' He asked wistfully.

'Not quite!' McKay answered. 'As you can tell from the highly irritating alarms, the city is in distress. The north pier is flooding and is erecting force fields to stop the spread of the deluge and therefore save the city from sinking.'

'Oh yeah like the Titanic!' Sheppard exclaimed excitedly.

McKay huffed noisily. 'Yes Sheppard, exactly like the Titanic.' He said patronisingly.

'But it didn't work for the Titanic!' Sheppard remembered. 'It kinda sunk! That's a bad plan!'

'Fortunately, the Atlantians were slightly more advanced than White Star Line so I'm sure it'll work this time!' McKay assured.

'Alright then.' Sheppard replied, not convinced. He remembered seeing that film and it didn't end well for most of the passengers including Leo!

'Could you tell me the position of my hostile so that I can kill him?' Sheppard asked pleasantly, he had decided to trust McKay that the city wasn't sinking under him.

'Have you not been listening to a word I've been saying? McKay shouted. 'Me and Zelenka are at this moment hurrying as fast as Radek's short legs will allow to the north pier!'

'You didn't tell me that!'

'Yes I did Sheppard; you just won't admit you weren't listening.'

'You didn't and I was listening, I heard all the huffing and puffing as well, I just didn't realise it was because you were doing physical exercise!' Sheppard retorted.

'That's Zelenka, not me!' McKay muttered defensively.

_Yeah right! _Sheppard thought, grinning. McKay couldn't even open a power bar without getting out of breath. Though thinking about it that could be more about excitement over his favourite food rather than exercise!

'Why are you going to the pier? I thought you said the city was handling it?' Sheppard asked.

'It is, unfortunately the city is saving what it sees as important areas and is sacrificing areas that it doesn't feel are as vital. The problem we have is our naqahdah generator that is in that area-'

'Let me guess,' Sheppard cut in 'it's not in a vital area and is in danger of getting a little wet?' Sheppard guessed sarcastically.

'That's right!' McKay sighed, why was his life never simple? 'The generator won't appreciate ah 'getting a little wet'. In other words it'll stop working!

'Zelenka and me are going to try and divert some of the force fields to protect the generator.' McKay explained simply.

'Alright but be careful McKay. The most important thing is the safety of Atlantis; we can always get new generators.' Sheppard warned.

'I know what I'm doing Sheppard, nothing will go wrong!' McKay promised.

Sheppard sighed, he had heard them words before, but McKay was more often right than wrong so Sheppard would just have to believe him. 'Keep me posted.' Sheppard ordered.

Sheppard looked up and down the corridor checking that the coast was clear. He then carried on the same way that he had been going before the explosion.

'Ronon, you there?' Sheppard asked, once again speaking into his radio.

'I'm here Sheppard.' Ronon replied calmly. 'I am on my way to assist you; I've taken out my hostiles.'

'That's a negative Ronon. I want you to head over to the gym. I left Doctor Weir on her own there and there's still one hostile at large.' Sheppard told him. 'Try and help her get our men out of the gym.'

'Understood.' Ronon replied.

Sheppard started walking down the corridor, his 9mm held out steadily in front of him in his good hand. The alarms made it hard to hear anything like the hostiles footsteps. He found that he was starting to get tired; the gun was getting heavier in his hand. The blood loss was finally catching up with him. Sheppard pushed his body on nevertheless, ignoring the warning signs that he needed rest.

The first that Sheppard knew that the hostile was behind him was when he was hit on the head with something blunt and heavy.

Sheppard painfully fell to the floor, jarring his shoulder and stomach wound. He slowly turned himself over, trying to clear his head of the stars that were circling it.

He looked up at the tall figure standing over him. It was the hostile he had been looking for but it looked like the hostile had found him instead.

Sheppard waited for the hostile's next move impatiently. He was too dizzy to even attempt to get up yet; he could probably add concussion to his list of injuries.

The hostile continued to stare at him unnervingly. Sheppard smiled at him from his position on the floor. 'So would you like to start or should I?' Sheppard asked politely.

The hostile stared down at Sheppard, a nasty grin appearing on his face. 'So this is the city of Atlantis' most fearsome warrior?' The hostile asked scornfully.

Sheppard frowned at this, the hostile couldn't mean what it sounded like he meant.

'Yes, I said the city of Atlantis! You may fool my underlings but you cannot fool me. This magnificent place could be nothing other than the destroyed city of Atlantis. Now it is obviously intact something that my gods will want to know above all else.' The hostile paused, checking that he had Sheppard's undivided attention.

_Great, _Sheppard thought _it's time for the bad guy explains his wicked plan before he kills you, which you always get in films! It's just so cliché! _'Look are you gonna yammer on all day?' Sheppard enquired.

The hostile gave him a dirty look and continued his speech. 'And when I tell them the news, I will be honoured above all others!'

Sheppard got to his feet unsteadily. 'You know I'm not going to let you leave without a fight so let's fight already!' He demanded.

'As you wish Atlantian warrior but I fear that it will not be much of a fight!' He looked at Sheppard's weakened state with amusement.

'You got that right!' Sheppard replied confidently. _I can take him!_ Sheppard tried to convince himself.

The hostile raised his long fighting pole that had given Sheppard his concussion a few minutes before.

Sheppard shakily raised his gun and without hesitation, he fired. The hostile quickly moved out of the path of the bullet. His pole swiftly snapped across Sheppard's extended arm, knocking the gun to the floor. Sheppard yelled in pain and cradled the injured arm to his chest.

The pole came at him again, this time hitting him on the torso, knocking the wind out of him. Sheppard had no answer for this man's strength or speed, not in his present condition.

Another blow came and another, forcing Sheppard once again to the floor. 'Say goodbye to your beloved city warrior! The wraith will destroy the city for good this time!' The hostile turned and walked away, in the direction of the control tower.

Sheppard lay, panting on the floor. At least a few bones were now definitely broken but Sheppard ignored this, instead focusing on the hostiles last words, 'destroy the city!'

'Like hell!' Sheppard grunted. He struggled to his feet and hobbled quickly after the hostile.

'Elizabeth!' Sheppard yelled into his radio as he got close to the control room. 'The last hostile is on route to the gate and I am in pursuit.'

Sheppard arrived in time to see the gate open with a rush. The hostile walked haughtily down the stairs towards the gate, smiling snidely at Sheppard before stepping through.

Sheppard ran quickly to the gate and dived through before it could shut off, injured and weapon less.

'John, wait for backup, do you hear? John?' Weir implored but the gate had already shut off behind him and Weir's plea was met with static.

**As usual please review if you have the time, you should see the smile I have on my face when I get the email with your comments! **


	6. Chapter 6: Through the Stargate

_Disclaimer: I don't own Stargate Atlantis or any of its characters just in case someone wants to sue!_

_Warning: There is strong violence in this story and scenes that some people may find upsetting so ye be warned!_

_Thank you to my beta The Bog Witch who corrected all my mistakes._

**Here's the next chapter. Again thanks for all the reviews. Hope you all enjoy this next chapter.**

Chapter Six: Through the Stargate

Sheppard fought to slow down his inertia once he had exited the stargate on the unknown world. His efforts came too late however, and he tumbled down the pesky steps that were often built leading up to a stargate.

Sheppard finished his bone jarring fall and landed on soft, sweet smelling grass. He groaned at the agonising pain. His body screamed to stay right where it was on its makeshift bed.

'I underestimated you warrior!' A malicious voice said above him. 'I didn't realise anyone would be stupid enough to run into certain death. You are unarmed and I would assume that you did not call for extra support from your fellow Atlantians?'

Sheppard ignored the rolling of his stomach and the various other stabs of pain up and down his body as he clambered to his feet. He took up a defensive stance, both arms held up in front of his chest, his hands in tight fists.

The hostile laughed at Sheppard and once again pulled out his fighting stick. He swung it expertly at Sheppard who tried valiantly to move out of its path.

He was too slow though and the pole came crashing down on his wounded shoulder. Sheppard bit down on his lip, trying to overcome the pain.

He shot his fist out at the hostile, before the pole could be swung at him again, and it connected with the man's gut. The hostile fell back slightly and Sheppard rallied, going in for another hit.

The hostile was ready for him though and swiped the pole at Sheppard's knees. Sheppard heard the crack that resonated through his entire body and the pain that accompanied it. He was sent crashing to the floor and from the dark spots that were appearing in his vision he knew that he was about finished in this fight.

_I'll be damned if I go alone! _Sheppard thought desperately. He didn't want the last thing that he did to be failing Atlantis and his friends.

He saw the shape moving towards him too late to even flinch. It hit him in the centre of his torso and he knew from the pain and the new tightness of his chest that the pole had wrecked severe damage.

He heard, rather than saw, the pole clatter to the floor and someone crouch beside him. His eyes were open but they were no longer processing what they saw. _That can't be good! _Sheppard thought dryly.

'I will end your pain now warrior. You fought nobly.' the hostile intoned sombrely. Sheppard felt the cold steel of the dagger against his vulnerable throat and reacted instinctively.

His arm reached out, groping the grass beside him until it fastened around the pole. He swung it upwards with as much force as he could muster in his weakened state, his vision clearing so that he could see the look of surprise on his adversary's face as his own weapon hit him on the head.

His eyes momentarily rolled back into his head and his grip on his dagger slackened.

Sheppard took the opportunity he had been gifted. He grabbed the sharp dagger and plunged it straight into the hostile's heart.

The hostile died with that look of surprise still on his face, unbelieving that a beaten opponent could defeat him.

Sheppard lay there for a few minutes, trying to gather the strength to push the dead man off of him but his body knew what his mind would not accept. He had endured too much and his body would no longer co-operate seeing now that Atlantis was safe.

XXXXX

Weir stood still for a moment listening to the static of her radio. Sheppard had obviously already gone through the gate, her order was too late.

She turned to Ronon who was standing guard at the end of the corridor. 'Ronon would you go to the control room and follow Sheppard?' She asked.

Ronon shifted uncomfortably. 'But Sheppard told me to stay with you.'

'I know but now I'm ordering you to help him. Don't worry I won't let you get in trouble, besides the Colonel needs your help.' Weir informed him.

Ronon nodded and went to leave. All of a sudden the Atlantian alarm became more high-pitched and a red flashing light started flashing on the ceiling above them. The doors at the end of the corridor slammed shut without any prompting from Weir or Ronon.

Weir sighed, it seemed to her that the city was going into lockdown but surely there wasn't another infectious disease in Atlantis. Well, Weir knew someone who may have something to do with the situation.

'Rodney? What's going on?' She asked, tapping her radio.

'Oh, ah hi Lizbeth.' McKay answered distractedly. 'There's er nothing to worry about. Everything's fine!'

'Rodney!' Weir said in a tone of voice that said that McKay had better tell her everything. She even crossed her arms, though McKay couldn't see her.

'Well we kind of ran into a slight problem when trying to save the generator.' McKay admitted grudgingly.

'What he means to say is that he took the force shields offline, against my better judgement, and that the city has responded by locking us out of the system.' Zelenka summed up.

'So Atlantis sensed a threat from McKay?' Weir wondered.

'Yes.' Zelenka offered easily.

'It's more complicated than that, I'll have you know.' McKay remarked angrily.

_It always is! _Weir thought wryly. 'Rodney! Focus! Sheppard is off-world and needs our help. How long until you can get the situation back under control?' Weir asked sharply, putting a calming hand on Ronon's shoulder, who was pacing restlessly.

'I don't know, I don't understand why it locked down in the first place!' McKay yelled, frustrated.

'But Doctor Zelenka said it was because of something that you did, just fix whatever did!' Weir replied, frowning.

'As ever, Elizabeth, it's not as simple as that!' McKay retorted.

'We will have it fixed within the hour, Doctor Weir!' Zelenka answered courteously.

Weir could hear McKay yelling something in the background to Zelenka, he had obviously turned his radio off, unwilling to talk to her any longer. 'Try your best.' Weir said to Zelenka, tapping her radio off.

She turned to Ronon. 'Don't worry, we'll help him soon!' She told him comfortingly.

Ronon nodded briefly before continuing his frantic pacing.

Weir sat down awkwardly on the floor of the corridor, she was so exhausted, the tiredness hitting her now that she had nothing pressing that she could be doing.

She couldn't stop her mind from wandering to what may be happening to Sheppard at that moment. He could be injured and in desperate need of their help and here she was sitting down doing nothing.

Over half an hour later the flashing lights and high-pitched alarms finally ceased.

'Doctor Weir, the city is stable again. The north pier is still flooded however. The city should be unlocked now.' Zelenka informed her.

Weir got to her feet stiffly. 'Yes it is Radek, thank you. Come back to the control room when you're finished, Rodney too!' Weir told him. She turned to the gym door and tried to open it. It remained defiantly closed. Weir felt close to tears. It seemed nothing would go right today.

Ronon came and stood next to Weir. 'Maybe we should try it my usual way?' He suggested.

Weir was confused. 'Your usual way?' She asked.

As an answer Ronon pulled out his gun and shot at the switch beside the gym door. Weir couldn't believe it as the door slid open revealing the missing soldiers.

She smiled slightly, McKay wouldn't be happy at the lack of respect Ronon had just displayed for Atlantian technology.

Lorne approached Weir relief plain on his face. 'Thanks for getting us out!' He said gratefully.

'That's alright Major, I want you to get your team geared up and be ready in the gateroom ASAP!' Weir ordered.

'Yes ma'am. May I ask where we're going?'

Weir suddenly looked distraught. 'Oh no how can we tell which planet John gated to?'

'The Colonel? Is he fit to be on duty?' Lorne asked.

'Probably not but there wasn't much choice as the city was under threat. How can we help Sheppard if no-one knows where he went?' She asked fitfully.

'Someone may know.' Ronon grunted.

'Who?' Weir asked, hope starting to blossom that they may yet save Sheppard.

'The prisoner.' he answered shortly.

Weir grinned happily. 'That sounds like a plan gentlemen! Major, Ronon and I will meet you in the control room in ten minutes.' She promised. She followed Ronon out of the gym at a quick march towards the brig.

When they arrived the prisoner got to his feet, not nearly as cocky as he had been acting earlier. He seemed to realise that The Chosen Twelve's plot had failed.

The SF was stood to attention at the door, staring guiltily at Weir's bandaged throat.

'Has he been co-operating since I was last here?' Weir asked the SF kindly.

'Yes ma'am except of that whole incident with you.' The SF replied formally.

Weir nodded thoughtfully and turned to the prisoner. 'Your friends are all dead or gone. You have nothing left to gain from staying loyal to the wraith. We can offer you a home on the mainland where you could grow crops in peace.

The prisoner seemed to wilt in front of her eyes. 'You would let me go free after what I did to you?'

'Yes, on one condition, one of my men followed your friend through the gate as he ran away. Where would your friend go?'

'And if I tell you, I get to go free?' The prisoner questioned carefully.

Weir nodded and the prisoner told them the gate address with no remorse in his voice.

Weir thanked him and hastily ran down the corridor towards the gate. Ronon followed reluctantly, he had been hoping to get some more payback for what The Chosen Twelve had done to his new friends.

They soon got to the control room to see Lorne's team ready to go. Beckett was also there with a team of nurses, Weir hoped that Sheppard wouldn't be needing them that badly.

Lorne came over to them. 'We're ready to depart ma'am apart from one thing. I'd like to ask Ronon to take Lieutenant Geller's place on this mission. I know that's what Geller would have wanted.' He had obviously just been told of his second in command's death.

Ronon agreed and went to wait with the rest of the team. Weir turned to Lorne. 'Bring the Colonel home Major.' Weir ordered.

'Will do Doctor Weir.' he answered confidently.

Weir walked up the steps that she had tumbled down with Sheppard so many hours before. She quickly dialled the correct address and waved as the four men walked through the stargate to find Sheppard, hopefully alive and no move injured than he had been when he had left.

**Please review if you have time. As always I love to read your comments. The next chapter will be the last one. Hope to have it up soon.**


	7. Chapter 7: Mea Culpa

_Disclaimer: I don't own Stargate Atlantis or any of its characters just in case someone wants to sue!_

_Warning: There is strong violence in this story and scenes that some people may find upsetting so ye be warned!_

_Thank you to my beta The Bog Witch who corrected all my mistakes._

**Hey sorry it took so long to get this chapter up. I spent longer researching the medical procedure but there still might be mistakes because I'm no doctor! Thanks for reading my story and thanks for all the great reviews, I have really enjoyed everyone's comments. Here's the last chapter:**

Chapter Seven: Mea Culpa

Lorne steadied himself as he exited the gate on the unknown planet. He looked around distrustfully. _'Trees and more trees!'_ He thought cynically, every planet they went to looked the same. His team came out of the stargate behind him followed by Ronon.

Lorne motioned to his team mates 'Spread out and keep an eye out for unfriendlies.' The two soldiers complied and they headed in different directions from the gate.

Ronon was hurrying down the steps and Lorne was quick to follow, assuming that the Saetadan had seen something. As they got closer Lorne could see the bulk of a body lying on the ground. He frowned slightly as he realised that it was the hostile.

Ronon knelt down and began to heave the body aside, it was then that Lorne saw the smaller figure of his CO.

'Oh thank God!' Lorne muttered. He bent down to help Ronon shift the weight. Lorne then gazed concerned at Sheppard who lay unmoving.

'He is alive.' Ronon remarked. He had his fingers pressed into Sheppard's neck.

Lorne quickly looked Sheppard over, assessing his injuries. Something wasn't quite right, there was a blue tinge to his lips and his breathing was very shallow. He looked at Sheppard's chest again and noticed the uneven rise and fall of his chest.

'Oh crap!' Lorne cursed. He quickly got to his feet and tapped frustrated on his ear piece. 'Atlantis, this is Major Lorne, we need a medical team here ASAP!'

'They're on their way now Major.' Weir's calming voice was transmitted into his ear. 'What's the Colonel's condition?'

Lorne sighed, knowing that this wasn't the news that Weir wanted to hear. 'Not good ma'am, the hostile is dead but Colonel Sheppard took quite a beating in the process.'

'Understood.' Weir replied.

Beckett burst through the open stargate and hurried over to where Lorne and Ronon knelt. 'How's our patient?' Beckett asked. He quickly felt for Sheppard's pulse. 'Weak and thready.' He murmured to himself. He carefully felt his patient's chest and ribcage. He shook his head. 'The things you manage to do to yourself!' He said to Sheppard. 'Nurse, pass me a needle.' He ordered.

'What's the prognosis doc?' Lorne wondered.

'Sheppard's condition is critical, I will try and stabilise him before we take him back to Atlantis.' Beckett tapped on his ear piece. 'Doctor Weir, please have a gurney waiting and have the operating room prepped. Please shut off the gate so that we can dial back.'

'Affirmative Doctor Beckett.' Came Weir's voice, she was obviously extremely worried about Sheppard though she tried to hide it. The gate shut off with a crack and Ronon hurried over to redial.

The nurse handed Beckett a large needle. Lorne noticed that it was empty. 'What's that for?' He asked.

'The colonel has a collapsed lung and his lung had filled with fluid and air, I will insert this needle to draw some of the fluids out so that we can get him back to Atlantis.' Beckett pulled the lid off the syringe. 'Hold him steady Major, don't worry he won't feel a thing, he's unconscious.'

Beckett cautiously inserted the needle into the side of Sheppard's chest that was not rising. There was no reaction from Sheppard, just as Beckett had promised. Beckett pulled the stopper up on the top of the syringe and Lorne flinched as he saw that it was full of fluid. He wasn't a doctor but he was sure that this wasn't a good sign.

'That's all that I can do for him here. Best get him to Atlantis sharpish.' Beckett suggested. He waved two medics over who were waiting with a stretcher. Lorne helped to gingerly move Sheppard onto the board, he was relieved to see that Beckett had improved his CO's condition, Sheppard was now breathing a little easier.

The medics picked the stretcher up and carried it through the gate, Beckett staying close to his patient all the way.

Lorne followed with Ronon and his two team mates, leaving the peaceful planet and the dead body behind. They stepped through the gate into the hustle and bustle of the control tower. Sheppard was being transferred to the gurney and being rushed toward the infirmary, Beckett was running to keep up with the fast moving gurney.

Weir quickly approached Lorne and Ronon. 'What happened to him Major? Ronon?' Her eyes were following the Doctor, she would rather be asking Beckett these questions.

'Sheppard killed the hostile, stabbed him in the heart.' Ronon supplied.

'So crisis over?' Weir asked.

The two men nodded slightly, it had been a close call this time.

'Alright, get checked out at the infirmary and get some rest, debrief in one hour.' The two men nodded again and set off for the infirmary followed by the rest of Lorne's team.

Weir was left alone in front of the gate. She slowly walked back to the stairs; it was time to tell the civilians that they could now leave their rooms again. Her eyes lingered on the pool of blood that was still at the foot of the stairs, it had been the worst day imaginable.

XXXXXXX

'He has a severe pneumothorax.' Beckett yelled to his fellow doctor as they entered the operating room. The doctor was already prepped and Beckett trusted the man trusted the man to keep Sheppard stable until Beckett scrubbed up.

When Beckett came back, Sheppard had an IV line set up and was intubated. 'I think the pneumothorax was caused by the lung being punctured by a broken rib.' Beckett informed his colleague. 'I will open him up to mend his lung. Keep an eye on his vitals.'

A few hours later Beckett walked exhaustedly out of the operating room and was unsurprised to see a crowd of people waiting anxiously outside. Weir was sitting in one of the chairs tentatively probing her neck. McKay was pacing up and down the hallway annoying Ronon, who was leaning against the wall cracking his knuckles menacingly whilst glaring at McKay. Even Teyla was there, resting in a chair next to Weir. Beckett frowned, he didn't remember giving Teyla permission to be out of bed. He decided to let it slide, for the moment anyway. He was sure that they were all waiting with bated breath to find out how Sheppard was doing. 'The operation was successful; I mended the damage to his lung. He is still intubated but I'm sure that he will be able to breath on his own soon. He has a few broken ribs, he has shattered his kneecap and bruised almost every part of his body. I'm sure that he has concussion but we won't know for sure until he wakes up. I also fixed the stitches that he pulled out in his shoulder. I don't know why I bother though I'm sure Colonel Sheppard will manage to get himself in some new trouble before I can even blink.'

'Does this mean that Colonel Sheppard will be alright?' Teyla asked.

'Aye lass, I'm confident that the Colonel will make a full recovery in time. He won't be out of the woods for a while yet.'

'Great so I guess he won't be able to help me fix the north pier? I need someone with a strong ATA gene to help with the repairs on the damages technology. Are we sure that he's not malingering?' McKay asked.

Beckett rolled his eyes. 'No Rodney, it's quite hard to fake a collapsed lung, not even you could fool me.' McKay looked like he was taking this as a challenge so Beckett quickly pressed on. 'Anyway, all go to your rooms to rest, that's an order, especially you Elizabeth, it's been a hard day. I will let you know when you can visit the Colonel. Teyla, you will come with me back to the hospital bed, I don't remember discharging you.' Beckett ordered.

Everyone hastily followed his orders, though McKay turned around and went to his lab as soon as Beckett was out of sight. Ronon set off toward the gym, even though he would have no sparring partner.

The next day Beckett allowed Weir to be Sheppard's first visitor. She walked into the room and was dismayed at the sight she saw. He was still intubated and had tubes coming out of different parts of his body.

'Don't worry lass. I know it looks shocking but John is fine. I set up a chest drain to get rid of the fluid from his lung. I hope to remove them in the next few hours if the Colonel shows signs of consciousness.'

'May I sit with him?' Weir asked hopefully.

'Of course. Call me if there's any change.'

Weir sat quietly with Sheppard, alone with her thoughts for the first time since the infiltration. There had been so much bloodshed today, so much pain for no reason.

Weir sat like this for some time even though there was so much paperwork she could be doing.

She was mid thought when some movement disturbed her in the bed next to her. Shepard was moving restlessly. 'Doctor Beckett!' Weir yelled.

Beckett quickly came out of his office. He checked Sheppard's vitals. 'He's starting to breath on his own, or trying to anyway. I'm going to remove the tubes now. You may not want to look Elizabeth.' Weir hastily looked away and only looked back when Beckett assured her it was safe to do so.

Sheppard looked much less scary without the tubes and Weir began to believe Beckett when he said that Sheppard would make a full recovery. 'He should wake up soon.' Beckett promised, going over to check on Teyla and his other patients.

Weir settled herself back into the chair beside Sheppard's bed. She didn't have long to wait however, within the hour Sheppard began to wake up.

He could feel someone's hand resting on top of his. _'That rules out Beckett, McKay and Ronon!'_ Sheppard thought dryly. _'Or I hope so; otherwise I have a slight problem!' _

He turned his head to look who was sitting in the chair. 'Hey,' he croaked.

'Hey!' Weir softly replied. She picked up the glass of water and put the straw to his lips. He gratefully sipped as much as he could and felt it sooth his raw throat.

'Deja vu!' He said.

'Yes.' Weir responded, remembering doing exactly the same thing for him yesterday. 'Beckett has been threatening to start charging rent because you're here so much.'

'Really?' Sheppard asked. 'Maybe I should start charging for saving the day, again!'

'Alright, alright. Please don't start keeping count like Rodney does.'

'Would I?' Sheppard asked innocently.

'Of course!' Weir remarked. She clasped her hands together nervously. 'John…' She started.

Sheppard immediately became serious. 'What is it?'

'We recovered Sergeant Smith's body from the north pier, I'm sorry it seems that he was caught in the explosion.' Weir had tears in her eyes.

Sheppard took in the news. Another man to die under his command, he would grieve for Geller and Smith later, in private but he could tell that Weir was taking it hard.

'What's the matter, Elizabeth?' Sheppard asked sympathetically. A tear rolled slowly down Weir's cheek. Sheppard took her hand in his. 'Hey, tell me.'

Weir sniffed and wiped her eyes, she hated self-pity but for some reason she couldn't help herself at the moment. 'Mea Culpa.' She said simply. She smiled at Sheppard's confused look. 'It's Latin.' She added. 'For-'

'My fault. I know what it means but what's your fault Elizabeth?' Sheppard asked.

'Geller, Smith, Teyla, you,' she listed.

'That's as much my fault as yours, Elizabeth, I wasn't here to help search which got Geller killed and I ordered Smith to the north pier which got him killed.'

'How do you deal with it?' Weir asked emotionally.

'You just do. What's this about Elizabeth? It's not like you. We have had men die under our command before.'

'I killed a man, John. I pulled the trigger and he died.' She answered sadly.

'Oh.' Sheppard said, remembering what had happened the day before. 'Listen, what you did wasn't pretty but it saved my life. You saved my life and I am very, very grateful.'

Weir nodded, feeling brighter, trying to look at it from a different point of view. 'I know, I will go and get Doctor Beckett, you must be in pain.'

'A little bit, yeah.' Sheppard admitted.

Later on that day McKay came to visit Sheppard. Sheppard grinned when he saw who it was. 'McKay! Can't believe you could tear yourself away from your lab long enough to visit me.'

'Er yeah, well just wanted to see how you were.' McKay replied awkwardly.

Sheppard suddenly saw that McKay was holding an ancient device. 'What do you want McKay?' Sheppard asked threateningly.

'Well er, I thought seeing as how you're on the mend, you could help me out in fixing the north pier, as it's your fault that it flooded.' McKay answered.

'How did you figure that out?' Sheppard asked. 'So you need someone with a strong ATA gene to touch things?'

'Yes I did just say that, why you insist on parroting everything back to me!'

Sheppard ignored his comment. 'I think I may have a solution for you that will make us both happy.

XXXXXXXX

A few days later after Sheppard had first woken up he was released from the infirmary long enough to go to the mainland for Lieutenant Geller and Sergeant Smith's memorial service. He had to promise to stay in Beckett's sight at all times and to eat more food to go but it was worth it to be finally flying again, not that he was the one piloting the jumper, that would be McKay, badly, but flying was flying he supposed.

The service was short, Weir said a few words about how brave and loyal the men were and a simple plaque was put on one of the trees just outside of the athosian village. It was just a gesture; their bodies had been sent back to Earth where they would have a full military funeral.

After the service, Weir came to help Sheppard back to the jumper. Sheppard leaned heavily on her arm and his walking stick to hobble back to where McKay and Beckett were waiting.

'John, do you remember the soldier who was guarding the prisoner when, well you know.' She was rubbing her neck nervously.

'Yes.' Sheppard answered cautiously.

'Well you know I asked you not to punish him.'

'Yes.'

'I was wondering if you kept your word.' Weir continued.

'Elizabeth, I am insulted that you don't trust me.' Sheppard protested, feigning innocence.

'Answer the question John, did you punish the soldier?'

'I may have slightly, but I had to Elizabeth, that's how the military works.' Sheppard explained.

'You didn't demote him, did you?' Weir asked.

'No, nothing like that. I know you didn't want him punished.' Sheppard explained mischievously. 'So I assigned him extra duties instead, helping McKay activate ancient devices, he has a very strong ATA gene, just like McKay wanted.'

'And this has nothing to do with the fact that it was a job you didn't want to do for yourself?' Weir asked thoughtfully.

'Let's just say it killed two birds with one stone!' Sheppard admitted.

The End

**Please review one last time I would love to hear what you all thought and if anyone has any ways they think I could improve my writing, you are more than welcome to pm or email me. **


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